Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016316.1 Corchorus olitorius cultivar O-4 contig16349, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 29629
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:197 original size:57 final size:56
Alignment explanation
Indices: 109--223 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 56
99 TATGCGTTTC
109 CTTTCACACAATAAATGTTATAATAAATCCTATCCCTCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCC-CCTATCTCTACTTAATTATT
* * *
166 CTTTCACATAATTAATGTTATATTAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
222 CT
1 CT
224 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 22 0.40
57 33 0.60
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
Found at i:1160 original size:25 final size:24
Alignment explanation
Indices: 1132--1193 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
1122 GTGGATTGTA
*
1132 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
1157 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
1181 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
1194 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:2494 original size:373 final size:379
Alignment explanation
Indices: 1862--2612 Score: 1406
Period size: 373 Copynumber: 2.0 Consensus size: 379
1852 TAAAGAAAAT
1862 TTGTAAAATTTAAACAATTTTATTTAAGGAATATTTTTAAAAATTGTAATATATCTAAGTTTTTT
1 TTGTAAAATTTAAACAATTTTATTTAAGGAATATTTTTAAAAATTGTAATATATCTAAGTTTTTT
1927 AATTAAATTAGTAAAATGGTAAAAAATAAAATAGGTATATAAATCAAAAAAATAGAGTTTTTATT
66 AATTAAATTAGTAAAATGGTAAAAAATAAAATAGGTATATAAAT-AAAAAAATAGAGTTTTTATT
1992 TTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTAAATATAAAAGTATAATTAAATAGTTATA
130 TTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTAAATATAAAAGTATAATTAAATAGTTATA
*
2057 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAAAC
195 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATTTAAAC
*
2122 AATGACATTTAAGAAATATATTCG-AAAATAAGGGTATAATGGACAGATATATACGAAAAATAAG
260 AATGACATTTAAGAAATATATTCGAAAAATAAGGATATAATGGACAGATATATACGAAAAATAAG
*
2186 GATATAATAGGTGATTCAAAAGTTTTACAAAACTCGTACTTTTATATATAGTAAA
325 GATATAATAGGTGATTCAAAAGTTTTACAAAACTCATACTTTTATATATAGTAAA
2241 TTGTAAAATTTAAACAATTTTATTTAAGGAATATTTTTAAAAATTGTAATATATCTAAGTTTTTT
1 TTGTAAAATTTAAACAATTTTATTTAAGGAATATTTTTAAAAATTGTAATATATCTAAGTTTTTT
2306 AATTAAATTAGTAAAATGGT-AAAAATAAAATAGGTATATAAAT-AAAAAATAGAGTTTTTA-TT
66 AATTAAATTAGTAAAATGGTAAAAAATAAAATAGGTATATAAATAAAAAAATAGAGTTTTTATTT
2368 TGAGTAAAACTATAAAAGTATATTT-AAAAATTCT-AATATAAAAGTATAATTAAATAGTTATAA
131 TGAGTAAAACTATAAAAGTATATTTAAAAAATTCTAAATATAAAAGTATAATTAAATAGTTATAA
2431 GGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATTTAAACA
196 GGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATTTAAACA
*
2496 ATGGCATTTAAGAAATATATTCGAAAAATAAGGATATAATGGACAGATATATACGAAAAATAAGG
261 ATGACATTTAAGAAATATATTCGAAAAATAAGGATATAATGGACAGATATATACGAAAAATAAGG
*
2561 ATATAATAGGTGATTCAAAAGTTTTACAAAACTCATAGTTTTATATATAGTA
326 ATATAATAGGTGATTCAAAAGTTTTACAAAACTCATACTTTTATATATAGTA
2613 TAGATGTATA
Statistics
Matches: 366, Mismatches: 5, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
373 115 0.31
374 99 0.27
375 27 0.07
376 17 0.05
378 23 0.06
379 85 0.23
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.36
Consensus pattern (379 bp):
TTGTAAAATTTAAACAATTTTATTTAAGGAATATTTTTAAAAATTGTAATATATCTAAGTTTTTT
AATTAAATTAGTAAAATGGTAAAAAATAAAATAGGTATATAAATAAAAAAATAGAGTTTTTATTT
TGAGTAAAACTATAAAAGTATATTTAAAAAATTCTAAATATAAAAGTATAATTAAATAGTTATAA
GGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATTTAAACA
ATGACATTTAAGAAATATATTCGAAAAATAAGGATATAATGGACAGATATATACGAAAAATAAGG
ATATAATAGGTGATTCAAAAGTTTTACAAAACTCATACTTTTATATATAGTAAA
Found at i:8673 original size:28 final size:30
Alignment explanation
Indices: 8642--8705 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
8632 CTCGAACCCG
* *
8642 CCTGACCCTAGA-A-CCGAGAGCCGAATGA
1 CCTGAACCTAGAGATCCGAAAGCCGAATGA
*
8670 CCTGAACCTAGATGATCCGAAATCCGAATGA
1 CCTGAACCTAGA-GATCCGAAAGCCGAATGA
8701 CCTGA
1 CCTGA
8706 GAAAATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
30 1 0.03
31 18 0.60
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.16
Consensus pattern (30 bp):
CCTGAACCTAGAGATCCGAAAGCCGAATGA
Found at i:9477 original size:21 final size:22
Alignment explanation
Indices: 9440--9480 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9430 GACAAACTCG
9440 TAACCCGAATAACCCAAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
9462 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
9481 TATTATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:10764 original size:22 final size:22
Alignment explanation
Indices: 10739--10785 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
10729 TTTTTAGTTG
*
10739 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
10761 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
10783 AGT
1 AGT
10786 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:10774 original size:93 final size:93
Alignment explanation
Indices: 10667--10846 Score: 308
Period size: 93 Copynumber: 1.9 Consensus size: 93
10657 TAGTATAGAT
*
10667 TAGTAATATCGTAAAAATAAAATA-TGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTT
1 TAGTAAAATCGTAAAAATAAAATAGT-TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTT
* *
10731 TTTAGTTGAGTAAAACTATAAAAGTAAAA
65 TTTAATTGACTAAAACTATAAAAGTAAAA
*
10760 TAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
1 TAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
10825 TTAATTGACTAAAACTATAAAA
66 TTAATTGACTAAAACTATAAAA
10847 ATTTAAACAA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 81 0.99
94 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAGTAAAATCGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
TTAATTGACTAAAACTATAAAAGTAAAA
Found at i:10920 original size:31 final size:31
Alignment explanation
Indices: 10882--10943 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
10872 ATATTCAAAA
*
10882 AATAAGGGTATAATAGGTGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
10913 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
10944 TACAAAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.31
Consensus pattern (31 bp):
AATAAGGGTATAATAGGCGATTCAAAAGTTT
Found at i:14228 original size:26 final size:26
Alignment explanation
Indices: 14199--14251 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
14189 TTATGTTACG
14199 ACTCGAAAGAAATTAATCTCAGATCA
1 ACTCGAAAGAAATTAATCTCAGATCA
* *
14225 ACTCGAAAGAGATTAATCTCGGATCA
1 ACTCGAAAGAAATTAATCTCAGATCA
14251 A
1 A
14252 TAAGACCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (26 bp):
ACTCGAAAGAAATTAATCTCAGATCA
Found at i:18554 original size:6 final size:6
Alignment explanation
Indices: 18545--18569 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18535 TCCTTTTAGT
18545 ACTAGA ACTAGA ACTAGA ACTAGA A
1 ACTAGA ACTAGA ACTAGA ACTAGA A
18570 TTCAACCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ACTAGA
Found at i:20526 original size:25 final size:25
Alignment explanation
Indices: 20498--20551 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
20488 TTTTACTGAT
20498 AAATTGTAGGAACATGGCAAAAACA
1 AAATTGTAGGAACATGGCAAAAACA
*
20523 AAATTGTAGGAACATGGCAAACACA
1 AAATTGTAGGAACATGGCAAAAACA
20548 AAAT
1 AAAT
20552 GTTTTCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.17
Consensus pattern (25 bp):
AAATTGTAGGAACATGGCAAAAACA
Found at i:23336 original size:3 final size:3
Alignment explanation
Indices: 23328--23353 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23318 ATAAAGGAAA
23328 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
23354 TGCCTGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:27471 original size:20 final size:20
Alignment explanation
Indices: 27446--27485 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27436 AATTACAAAC
27446 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
27466 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
27486 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:27977 original size:79 final size:79
Alignment explanation
Indices: 27846--28005 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
27836 AATGGAAATG
27846 CAGGTTTTCACTTGGAGAGAGAAATTTAATCCAAAATTTTAATGAGTTCATCCAACCACCCTTCT
1 CAGGTTTTCACTTGGAGAGAGAAATTTAATCCAAAATTTTAATGAGTTCATCCAACCACCCTTCT
27911 CTCTTTGTAGGCCC
66 CTCTTTGTAGGCCC
27925 CAGGTTTTCACTTGGAGAGAGAAATTTAATCCAAAATTTTAATGAGTTCATCCAACCACCCTTCT
1 CAGGTTTTCACTTGGAGAGAGAAATTTAATCCAAAATTTTAATGAGTTCATCCAACCACCCTTCT
27990 CTCTTTGTAGGCCC
66 CTCTTTGTAGGCCC
28004 CA
1 CA
28006 TTATTTTCTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (79 bp):
CAGGTTTTCACTTGGAGAGAGAAATTTAATCCAAAATTTTAATGAGTTCATCCAACCACCCTTCT
CTCTTTGTAGGCCC
Found at i:28115 original size:12 final size:10
Alignment explanation
Indices: 28079--28121 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
28069 TTAATTACTC
*
28079 TATAATTTAT
1 TATATTTTAT
*
28089 TATATTTTCT
1 TATATTTTAT
28099 TATATTCCTTAT
1 TATATT--TTAT
28111 TATATTTTAT
1 TATATTTTAT
28121 T
1 T
28122 TAATATACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 19 0.68
12 9 0.32
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (10 bp):
TATATTTTAT
Done.